One more way to parse the sequence. The initialization statement is only needed if zero-counts must be defined.

use strict;
use warnings;
use Readonly;
use Data::Dumper qw( Dumper );
Readonly::Scalar my $seq => "ATCGGCGCCTAT" ;
my %count;
@count{ qw(A1 A2 A3 T1 T2 T3 C1 C2 C3 G1 G2 G3 ) } = (0) x (3*4); 
foreach my $i (0 .. length($seq)-1 ) {
    my $pos = $i % 3 + 1;
    my $base = substr $seq, $i, 1;
    $count{$base.$pos}++;
}

$Data::Dumper::Sortkeys = 1;
print Dumper \%count;
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Or if you really want individual scalar counts and do not mind global variables or symbolic references.

use strict;
use warnings;
my $seq = 'ATCGGCGCCTAT' ;
my %count;
our( $A1, $A2, $A3, $T1, $T2, $T3, $C1, $C2, $C3, $G1, $G2, $G3 )
    = (0) x 12;
foreach my $i (0 .. length($seq)-1 ) {
    my $pos = $i % 3 + 1;
    my $base = substr $seq, $i, 1;
    {no strict 'refs'; ${$base.$pos}++;}
}

print $A1, $A2, $A3, $T1, $T2, $T3, $C1, $C2, $C3, $G1, $G2, $G3; 
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